Microbial biomass nitrogen and carbon were studied in long-term field experiments with continuous cultivation of silage maize and with crop rotation. A positive effect of organic fertilizers on the microbial biomass nitrogen and the carbon content in soil was observed. Statistically significant effect of organic fertilizers on the higher content of microbial biomass C and N was established in the first year after their application. During the application the content of microbial biomass carbon and nitrogen decreased, but there were higher biomass C and N contents compared to control, even without statistical significance. A negative effect on microbial biomass carbon and nitrogen content in soil came from the application of mineral nitrogen fertilizers in experiments with maize. Statistically significant effect of mineral N fertilizers was observed after their application. In the course of the N fertilizers application the content of microbial biomass carbon and nitrogen was lower than control. No statistically significant effects of mineral nitrogen fertilizers on the microbial biomass nitrogen and carbon content were observed in field experiments with crop rotation over the eight years of experiment duration. The higher effect of mineral and organic fertilizers application on the changes in microbial biomass C and N was reported in experiments with continuous cultivation of maize compared to experiments with crop rotation.